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trunc_seq ========= `trunc_seq.pl` is a script to truncate sequence files. * [Synopsis](#synopsis) * [Description](#description) * [Usage](#usage) * [Options](#options) * [Output](#output) * [Run environment](#run-environment) * [Dependencies](#dependencies) * [Author - contact](#author---contact) * [Citation, installation, and license](#citation-installation-and-license) * [Changelog](#changelog) ## Synopsis perl trunc_seq.pl 20 3500 seq-file.embl > seq-file_trunc_20_3500.embl **or** perl trunc_seq.pl file_of_filenames_and_coords.tsv ## Description This script truncates sequence files according to the given coordinates. The features/annotations in RichSeq files (e.g. EMBL or GENBANK format) will also be adapted accordingly. Use option **-o** to specify a different output sequence format. Input can be given directly as a file and truncation coordinates to the script, with the start position as the first argument, stop as the second and (the path to) the sequence file as the third. In this case the truncated sequence entry is printed to *STDOUT*. Input sequence files should contain only one sequence entry, if a multi-sequence file is used as input only the **first** sequence entry is truncated. Alternatively, a file of filenames (fof) with respective coordinates and sequence files in the following **tab-separated** format can be given to the script (the header is optional): \#start stop seq-file<br> 300 9000 (path/to/)seq-file<br> 50 1300 (path/to/)seq-file2<br> With a fof the resulting truncated sequence files are printed into a results directory. Use option **-r** to specify a different results directory than the default. It is also possible to truncate a RichSeq sequence file loaded into the [Artemis](http://www.sanger.ac.uk/science/tools/artemis) genome browser from the Sanger Institute: Select a subsequence and then go to Edit -> Subsequence (and Features) ## Usage perl trunc_seq.pl -o gbk 120 30000 seq-file.embl > seq-file_trunc_120_3000.gbk **or** perl trunc_seq.pl -o fasta 5300 18500 seq-file.gbk | perl revcom_seq.pl -i fasta > seq-file_trunc_revcom.fasta **or** perl trunc_seq.pl -r path/to/trunc_embl_dir -o embl file_of_filenames_and_coords.tsv ## Options - **-h**, **-help** Help (perldoc POD) - **-o**=*str*, **-outformat**=*str* Specify different sequence format for the output (files) [fasta, embl, or gbk] - **-r**=*str*, **-result\_dir**=*str* Path to result folder for fof input \[default = './trunc\_seq\_results'\] - **-v**, **-version** Print version number to *STDOUT* ## Output - *STDOUT* If a single sequence file is given to the script the truncated sequence file is printed to *STDOUT*. Redirect or pipe into another tool as needed. **or** - ./trunc_seq_results If a fof is given to the script, all output files are stored in a results folder - ./trunc_seq_results/seq-file_trunc_start_stop.format Truncated output sequence files are named appended with 'trunc' and the corresponding start and stop positions ## Run environment The Perl script runs under Windows and UNIX flavors. ## Dependencies - [**BioPerl**](http://www.bioperl.org) (tested version 1.007001) ## Author - contact Andreas Leimbach (aleimba[at]gmx[dot]de; Microbial Genome Plasticity, Institute of Hygiene, University of Muenster) ## Citation, installation, and license For [citation](https://github.com/aleimba/bac-genomics-scripts#citation), [installation](https://github.com/aleimba/bac-genomics-scripts#installation-recommendations), and [license](https://github.com/aleimba/bac-genomics-scripts#license) information please see the repository main [*README.md*](https://github.com/aleimba/bac-genomics-scripts/blob/master/README.md). ## Changelog * v0.2 (2015-12-07) * Merged funtionality of `trunc_seq.pl` and `run_trunc_seq.pl` in one single script * Allows now single file and file of filenames (fof) with coordinates input * output for single file input printed to *STDOUT* now * output for fof input printed into files in a result directory, new option **-r** to specify result directory * included a POD instead of a simple usage text * included `pod2usage` with Pod::Usage * included 'use autodie' pragma * options with Getopt::Long * output format now specified with option **-o** * included version switch, **-v** * fixed bug to remove input filepaths from fof input for output files * skip empty or comment lines (/^#/) in fof input * check and warn if input seq file has more than one seq entries * v0.1 (2013-02-08) * In v0.1 `trunc_seq.pl` only for single sequence input, but included additional wrapper script `run_trunc_seq.pl` for a fof input